This is an R Markdown document that checks data that has passed initial delivery QC and is now in the test phase.
When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document.
Uses check_fields() function to control if all required fields are present.
check_Chlorophyll(myfile)## All required fields present## # A tibble: 0 x 0## Rows: 10
## Columns: 70
## $ delivery_datatype <fct> Chlorophyll, Chlorophyll, Chloro...
## $ check_status_sv <fct> Klar, Klar, Klar, Klar, Klar, Kl...
## $ data_checked_by_sv <fct> Leverantör, Leverantör, Leverant...
## $ visit_year <int> 2007, 2007, 2007, 2007, 2007, 20...
## $ station_name <fct> K382, K390 / U, K336 / G, K390 /...
## $ reported_station_name <fct> K382, K390, K336, K390, K333, K3...
## $ sample_location_id <int> NA, 159417, 159416, 159417, 1594...
## $ station_id <int> NA, 188696, 188695, 188696, 1886...
## $ sample_project_name_sv <fct> Coordinated recipient monitoring...
## $ sample_orderer_name_sv <fct> Ljusnan-Voxnan Coalition of Wate...
## $ platform_code <int> 7798, 7798, 7798, 7798, 7798, 77...
## $ visit_id <int> 6011, 6012, 6008, 6018, 6013, 60...
## $ expedition_id <lgl> NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ shark_sample_id_md5 <fct> 0100b4fc85c96cf3f7f4bbb2deec1b24...
## $ sample_date <date> 2007-07-10, 2007-07-10, 2007-07...
## $ sample_time <lgl> NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ sample_enddate <lgl> NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ sample_endtime <lgl> NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ sample_latitude_dm <fct> 61 11.09, 61 12.27, 61 16.65, 61...
## $ sample_longitude_dm <fct> 17 11.52, 17 09.17, 17 09.97, 17...
## $ sample_latitude_dd <dbl> 61.18483, 61.20450, 61.27750, 61...
## $ sample_longitude_dd <dbl> 17.19200, 17.15283, 17.16617, 17...
## $ positioning_system_code <lgl> NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ water_depth_m <lgl> NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ wind_direction_code <int> 18, 22, 12, 13, 14, 12, 13, 13, ...
## $ wind_speed_ms <int> 2, 2, 6, 4, 5, 3, 3, 2, 7, 6
## $ air_temperature_degc <lgl> NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ air_pressure_hpa <lgl> NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ weather_observation_code <int> 9, 9, 9, 9, 9, 9, 9, 9, 9, 9
## $ cloud_observation_code <int> 9, 9, 9, 9, 9, 9, 9, 9, 9, 9
## $ wave_observation_code <int> 9, 9, 9, 9, 9, 9, 9, 9, 9, 9
## $ ice_observation_code <int> 9, 9, 9, 9, 9, 9, 9, 9, 9, 9
## $ secchi_depth_m <lgl> NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ secchi_depth_quality_flag <lgl> NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ visit_comment <lgl> NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ sample_id <lgl> NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ sample_min_depth_m <int> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
## $ sample_max_depth_m <int> 10, 10, 6, 10, 4, 2, 6, 2, 10, 4
## $ sampling_laboratory_name_sv <fct> Alcontrol laboratories, Alcontro...
## $ sampling_laboratory_accreditated <lgl> NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ sampler_type_code <fct> HOS, HOS, HOS, HOS, HOS, HOS, HO...
## $ sampled_volume_l <lgl> NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ sample_comment <lgl> NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ parameter <fct> Chlorophyll-a, Chlorophyll-a, Ch...
## $ value <dbl> 3.3, 3.1, 5.0, 2.0, 1.8, 6.0, 5....
## $ unit <fct> ug/l, ug/l, ug/l, ug/l, ug/l, ug...
## $ quality_flag <lgl> NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ calc_by_dc <lgl> NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ analysis_method_code <lgl> NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ method_documentation <lgl> NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ method_reference_code <fct> SS 028146-1 mod, SS 028146-1 mod...
## $ variable_comment <lgl> NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ estimation_uncertainty <lgl> NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ method_calculation_uncertainty <lgl> NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ quantification_limit <lgl> NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ detection_limit <lgl> NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ analysis_range <lgl> NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ analytical_laboratory_name_sv <fct> Alcontrol laboratories, Alcontro...
## $ analytical_laboratory_accreditated <lgl> NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ analysis_date <lgl> NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ station_viss_eu_id <fct> NA, SE678840-157245, SE679655-15...
## $ water_land_station_type_code <lgl> NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ monitoring_station_type_code <lgl> NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ monitoring_purpose_code <lgl> NA, NA, NA, NA, NA, NA, NA, NA, ...
## $ monitoring_program_code <fct> REG, REG, REG, REG, REG, REG, RE...
## $ reporting_institute_name_sv <fct> Swedish Meteorological and Hydro...
## $ data_holding_centre <fct> Swedish Meteorological and Hydro...
## $ internet_access <fct> "http://sharkweb.smhi.se, http:/...
## $ dataset_name <fct> SHARK_Chlorophyll_2007_SMHI_LVVF...
## $ dataset_file_name <fct> SHARK_Chlorophyll_2007_SMHI_LVVF...Uses plot_map_leaflet to render an interactive leaflet map of sampled stations in the data.
Uses check_onland() to control if any locations are on land.
# check_onland(myfile)Uses check_depth() to control if any sample depths are incorrect.
# check_depth(myfile)Uses check_outliers() function to control if all values are within range.
check_chlorophyll_conc(myfile)Uses check_logical() function to control if data follows logical assumptions.
check_value_logical(myfile)## Expected numerical value is formatted as numerical and no character values were foundUses check_codes() function to control if data follows the SMHI codelist.
check_code_proj(myfile)##
## -- Column specification --------------------------------------------------------
## cols(
## Data_field = col_character(),
## Code = col_character(),
## `Beskrivning/Svensk översättning` = col_character(),
## `Description/English translate` = col_character()
## )## All project (PROJ) codes found# Date time
Sys.time()## [1] "2020-11-11 21:25:11 EET"# Here we store the session info for this script
sessioninfo::session_info()## - Session info ---------------------------------------------------------------
## setting value
## version R version 4.0.3 (2020-10-10)
## os Windows 10 x64
## system x86_64, mingw32
## ui RTerm
## language (EN)
## collate Swedish_Sweden.1252
## ctype Swedish_Sweden.1252
## tz Europe/Helsinki
## date 2020-11-11
##
## - Packages -------------------------------------------------------------------
## package * version date lib source
## assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.3)
## backports 1.2.0 2020-11-02 [1] CRAN (R 4.0.3)
## broom 0.7.2 2020-10-20 [1] CRAN (R 4.0.3)
## cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.0.3)
## cli 2.1.0 2020-10-12 [1] CRAN (R 4.0.3)
## colorspace 2.0-0 2020-11-11 [1] CRAN (R 4.0.3)
## crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.3)
## crosstalk 1.1.0.1 2020-03-13 [1] CRAN (R 4.0.3)
## data.table 1.13.2 2020-10-19 [1] CRAN (R 4.0.3)
## DBI 1.1.0 2019-12-15 [1] CRAN (R 4.0.3)
## dbplyr 2.0.0 2020-11-03 [1] CRAN (R 4.0.3)
## digest 0.6.27 2020-10-24 [1] CRAN (R 4.0.3)
## dplyr * 1.0.2 2020-08-18 [1] CRAN (R 4.0.3)
## DT * 0.16 2020-10-13 [1] CRAN (R 4.0.3)
## ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.3)
## evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.3)
## fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.3)
## forcats * 0.5.0 2020-03-01 [1] CRAN (R 4.0.3)
## fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.3)
## generics 0.1.0 2020-10-31 [1] CRAN (R 4.0.3)
## ggplot2 * 3.3.2 2020-06-19 [1] CRAN (R 4.0.3)
## glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.3)
## gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.3)
## haven 2.3.1 2020-06-01 [1] CRAN (R 4.0.3)
## hms 0.5.3 2020-01-08 [1] CRAN (R 4.0.3)
## htmltools 0.5.0 2020-06-16 [1] CRAN (R 4.0.3)
## htmlwidgets 1.5.2 2020-10-03 [1] CRAN (R 4.0.3)
## httr * 1.4.2 2020-07-20 [1] CRAN (R 4.0.3)
## jsonlite 1.7.1 2020-09-07 [1] CRAN (R 4.0.3)
## knitr * 1.30 2020-09-22 [1] CRAN (R 4.0.3)
## labeling 0.4.2 2020-10-20 [1] CRAN (R 4.0.3)
## lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.0.3)
## leaflet * 2.0.3 2019-11-16 [1] CRAN (R 4.0.3)
## leaflet.providers 1.9.0 2019-11-09 [1] CRAN (R 4.0.3)
## lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.3)
## lubridate * 1.7.9 2020-06-08 [1] CRAN (R 4.0.3)
## magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.3)
## modelr 0.1.8 2020-05-19 [1] CRAN (R 4.0.3)
## munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.3)
## pillar 1.4.6 2020-07-10 [1] CRAN (R 4.0.3)
## pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.3)
## plotly * 4.9.2.1 2020-04-04 [1] CRAN (R 4.0.3)
## purrr * 0.3.4 2020-04-17 [1] CRAN (R 4.0.3)
## R6 2.5.0 2020-10-28 [1] CRAN (R 4.0.3)
## rappdirs 0.3.1 2016-03-28 [1] CRAN (R 4.0.3)
## Rcpp 1.0.5 2020-07-06 [1] CRAN (R 4.0.3)
## readr * 1.4.0 2020-10-05 [1] CRAN (R 4.0.3)
## readxl * 1.3.1 2019-03-13 [1] CRAN (R 4.0.3)
## reprex 0.3.0 2019-05-16 [1] CRAN (R 4.0.3)
## rlang 0.4.8 2020-10-08 [1] CRAN (R 4.0.3)
## rmarkdown 2.5 2020-10-21 [1] CRAN (R 4.0.3)
## rstudioapi 0.12 2020-11-10 [1] CRAN (R 4.0.3)
## rvest 0.3.6 2020-07-25 [1] CRAN (R 4.0.3)
## scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.3)
## sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.3)
## SHARK4R * 0.0.1 2020-11-11 [1] Github (sharksmhi/SHARK4R@68a0e0f)
## stringi 1.5.3 2020-09-09 [1] CRAN (R 4.0.3)
## stringr * 1.4.0 2019-02-10 [1] CRAN (R 4.0.3)
## tibble * 3.0.4 2020-10-12 [1] CRAN (R 4.0.3)
## tidyr * 1.1.2 2020-08-27 [1] CRAN (R 4.0.3)
## tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.3)
## tidyverse * 1.3.0 2019-11-21 [1] CRAN (R 4.0.3)
## utf8 1.1.4 2018-05-24 [1] CRAN (R 4.0.3)
## vctrs 0.3.4 2020-08-29 [1] CRAN (R 4.0.3)
## viridisLite 0.3.0 2018-02-01 [1] CRAN (R 4.0.3)
## withr 2.3.0 2020-09-22 [1] CRAN (R 4.0.3)
## worrms * 0.4.2 2020-07-08 [1] CRAN (R 4.0.3)
## xfun 0.19 2020-10-30 [1] CRAN (R 4.0.3)
## xml2 1.3.2 2020-04-23 [1] CRAN (R 4.0.3)
## yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.3)
##
## [1] C:/__R/R-4.0.3/library## Time difference of 5.114347 secs